Starting phenix.real_space_refine on Fri Mar 6 16:18:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pp8_20422/03_2026/6pp8_20422_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pp8_20422/03_2026/6pp8_20422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pp8_20422/03_2026/6pp8_20422_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pp8_20422/03_2026/6pp8_20422_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pp8_20422/03_2026/6pp8_20422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pp8_20422/03_2026/6pp8_20422.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 35 5.16 5 C 10120 2.51 5 N 2720 2.21 5 O 3209 1.98 5 H 16234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32335 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5273 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 2 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5409 Classifications: {'peptide': 351} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain breaks: 1 Chain: "C" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5396 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "D" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5377 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5395 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 2 Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5244 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 59 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.22, per 1000 atoms: 0.19 Number of scatterers: 32335 At special positions: 0 Unit cell: (146.16, 140.36, 102.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 17 15.00 O 3209 8.00 N 2720 7.00 C 10120 6.00 H 16234 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 957.4 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 53.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.706A pdb=" N ASP A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.790A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 158 through 170 removed outlier: 4.101A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.540A pdb=" N ILE A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.642A pdb=" N GLN A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.583A pdb=" N GLY A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 4.066A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.891A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 299' Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.514A pdb=" N ARG A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.679A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.547A pdb=" N LEU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.815A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.580A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.915A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.791A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.565A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.692A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.506A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.577A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.597A pdb=" N ASP B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 195 " --> pdb=" O LYS B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.926A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.707A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.737A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.598A pdb=" N ARG B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.570A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.838A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.735A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.779A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.726A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.809A pdb=" N LYS C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.542A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 4.161A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.508A pdb=" N LYS C 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.904A pdb=" N GLN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.829A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.868A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.673A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 removed outlier: 3.770A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.648A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.717A pdb=" N LEU C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.006A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.638A pdb=" N ALA C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.844A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.706A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.906A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.618A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.543A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.877A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.927A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.716A pdb=" N ALA D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.605A pdb=" N LEU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.753A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.691A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 removed outlier: 3.675A pdb=" N LEU D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.529A pdb=" N LEU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.742A pdb=" N ALA D 379 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.661A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.674A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 101 Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.524A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.553A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.553A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.652A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.554A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.783A pdb=" N ILE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 343 removed outlier: 3.685A pdb=" N LEU E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 removed outlier: 4.085A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 371 Processing helix chain 'E' and resid 372 through 380 removed outlier: 3.601A pdb=" N VAL E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 399 through 405 removed outlier: 3.867A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.577A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 102 removed outlier: 3.578A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.640A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 4.126A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 204 through 217 removed outlier: 4.199A pdb=" N GLN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.607A pdb=" N GLY F 227 " --> pdb=" O PRO F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 removed outlier: 4.072A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.989A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.635A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.761A pdb=" N ARG F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 332 through 345 removed outlier: 4.031A pdb=" N LEU F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.588A pdb=" N LEU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 356 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.547A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.831A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 182 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 115 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.917A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.630A pdb=" N ASP B 184 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.864A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 222 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.760A pdb=" N ILE B 398 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 3.672A pdb=" N THR C 141 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 182 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 349 through 350 removed outlier: 4.019A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 143 through 144 removed outlier: 3.714A pdb=" N ASP D 184 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.062A pdb=" N LYS D 395 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 144 removed outlier: 3.633A pdb=" N ALA E 143 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP E 184 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.943A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 347 through 348 removed outlier: 6.872A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 140 through 144 removed outlier: 3.745A pdb=" N THR F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL F 181 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.859A pdb=" N ALA F 220 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 238 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 395 through 397 removed outlier: 3.513A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 16228 1.05 - 1.27: 2877 1.27 - 1.50: 6185 1.50 - 1.72: 7192 1.72 - 1.95: 59 Bond restraints: 32541 Sorted by residual: bond pdb=" N SER B 62 " pdb=" H1 SER B 62 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N GLU D 234 " pdb=" CA GLU D 234 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.29e-02 6.01e+03 7.54e+00 bond pdb=" N PHE D 235 " pdb=" H PHE D 235 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C VAL C 238 " pdb=" N ASP C 239 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.29e-02 6.01e+03 6.58e+00 bond pdb=" N LEU D 236 " pdb=" CA LEU D 236 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.53e+00 ... (remaining 32536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 57965 1.86 - 3.71: 1067 3.71 - 5.57: 127 5.57 - 7.42: 12 7.42 - 9.28: 3 Bond angle restraints: 59174 Sorted by residual: angle pdb=" N ALA F 151 " pdb=" CA ALA F 151 " pdb=" C ALA F 151 " ideal model delta sigma weight residual 111.24 119.64 -8.40 1.38e+00 5.25e-01 3.71e+01 angle pdb=" N SER E 266 " pdb=" CA SER E 266 " pdb=" C SER E 266 " ideal model delta sigma weight residual 109.72 115.67 -5.95 1.60e+00 3.91e-01 1.38e+01 angle pdb=" N GLY F 265 " pdb=" CA GLY F 265 " pdb=" C GLY F 265 " ideal model delta sigma weight residual 113.18 104.69 8.49 2.37e+00 1.78e-01 1.28e+01 angle pdb=" CA GLN D 233 " pdb=" C GLN D 233 " pdb=" O GLN D 233 " ideal model delta sigma weight residual 121.84 117.87 3.97 1.16e+00 7.43e-01 1.17e+01 angle pdb=" O VAL C 238 " pdb=" C VAL C 238 " pdb=" N ASP C 239 " ideal model delta sigma weight residual 122.97 119.89 3.08 9.00e-01 1.23e+00 1.17e+01 ... (remaining 59169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13561 17.86 - 35.71: 1133 35.71 - 53.57: 307 53.57 - 71.43: 69 71.43 - 89.28: 8 Dihedral angle restraints: 15078 sinusoidal: 8574 harmonic: 6504 Sorted by residual: dihedral pdb=" CD ARG D 307 " pdb=" NE ARG D 307 " pdb=" CZ ARG D 307 " pdb=" NH1 ARG D 307 " ideal model delta sinusoidal sigma weight residual 0.00 32.18 -32.18 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CA ASP E 137 " pdb=" CB ASP E 137 " pdb=" CG ASP E 137 " pdb=" OD1 ASP E 137 " ideal model delta sinusoidal sigma weight residual -30.00 -83.64 53.64 1 2.00e+01 2.50e-03 9.77e+00 dihedral pdb=" CB GLU D 285 " pdb=" CG GLU D 285 " pdb=" CD GLU D 285 " pdb=" OE1 GLU D 285 " ideal model delta sinusoidal sigma weight residual 0.00 84.76 -84.76 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 15075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1751 0.034 - 0.067: 542 0.067 - 0.101: 191 0.101 - 0.134: 111 0.134 - 0.168: 14 Chirality restraints: 2609 Sorted by residual: chirality pdb=" CA LEU D 236 " pdb=" N LEU D 236 " pdb=" C LEU D 236 " pdb=" CB LEU D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ILE F 301 " pdb=" N ILE F 301 " pdb=" C ILE F 301 " pdb=" CB ILE F 301 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ILE E 301 " pdb=" N ILE E 301 " pdb=" C ILE E 301 " pdb=" CB ILE E 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 2606 not shown) Planarity restraints: 4828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 307 " 0.600 9.50e-02 1.11e+02 2.00e-01 4.23e+01 pdb=" NE ARG D 307 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 307 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 307 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 307 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG D 307 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG D 307 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG D 307 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 307 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 123 " -0.029 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C SER E 123 " 0.101 2.00e-02 2.50e+03 pdb=" O SER E 123 " -0.038 2.00e-02 2.50e+03 pdb=" N GLY E 124 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.325 9.50e-02 1.11e+02 1.08e-01 1.24e+01 pdb=" NE ARG A 98 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.007 2.00e-02 2.50e+03 ... (remaining 4825 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 151 2.02 - 2.67: 47795 2.67 - 3.31: 90896 3.31 - 3.96: 111576 3.96 - 4.60: 177381 Nonbonded interactions: 427799 Sorted by model distance: nonbonded pdb=" HH TYR F 96 " pdb=" O ARG F 178 " model vdw 1.379 2.450 nonbonded pdb=" O GLU B 263 " pdb=" HG1 THR B 264 " model vdw 1.450 2.450 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.463 2.450 nonbonded pdb=" HZ3 LYS F 125 " pdb=" O1B ADP F 600 " model vdw 1.493 2.450 nonbonded pdb=" O LEU B 326 " pdb=" HG1 THR B 334 " model vdw 1.540 2.450 ... (remaining 427794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'B' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'C' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'D' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'E' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'F' and (resid 65 through 192 or resid 201 through 227 or resid 233 throu \ gh 259 or (resid 260 and (name N or name CA or name C or name O or name CB or na \ me CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or na \ me HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 261 through 41 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 30.890 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16308 Z= 0.168 Angle : 0.720 9.280 22075 Z= 0.400 Chirality : 0.043 0.168 2609 Planarity : 0.007 0.258 2840 Dihedral : 12.437 89.282 6194 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2047 helix: -1.87 (0.15), residues: 728 sheet: -1.64 (0.27), residues: 272 loop : -1.20 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.017 0.001 TYR F 96 PHE 0.008 0.001 PHE A 140 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00347 (16307) covalent geometry : angle 0.72012 (22075) hydrogen bonds : bond 0.31071 ( 594) hydrogen bonds : angle 8.24533 ( 1671) Misc. bond : bond 0.02214 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7941 (t80) cc_final: 0.7626 (t80) REVERT: A 245 PHE cc_start: 0.5181 (m-80) cc_final: 0.4942 (m-80) REVERT: A 287 LEU cc_start: 0.8856 (mt) cc_final: 0.8632 (mp) REVERT: A 317 LEU cc_start: 0.7186 (mt) cc_final: 0.6917 (mt) REVERT: B 140 PHE cc_start: 0.7262 (t80) cc_final: 0.5583 (t80) REVERT: B 141 THR cc_start: 0.9447 (t) cc_final: 0.8968 (p) REVERT: B 279 ASP cc_start: 0.8742 (m-30) cc_final: 0.8401 (t0) REVERT: B 293 GLU cc_start: 0.9011 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 393 VAL cc_start: 0.8875 (t) cc_final: 0.8625 (t) REVERT: C 136 LEU cc_start: 0.8758 (tp) cc_final: 0.8483 (tp) REVERT: C 294 ASP cc_start: 0.8891 (m-30) cc_final: 0.8658 (m-30) REVERT: C 319 GLU cc_start: 0.8956 (pt0) cc_final: 0.8724 (pm20) REVERT: C 352 ASP cc_start: 0.8824 (p0) cc_final: 0.8321 (t0) REVERT: C 366 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9237 (mmmt) REVERT: D 130 GLU cc_start: 0.9107 (tt0) cc_final: 0.8331 (tm-30) REVERT: D 182 TYR cc_start: 0.8926 (t80) cc_final: 0.8327 (t80) REVERT: D 201 ASP cc_start: 0.8918 (m-30) cc_final: 0.8409 (p0) REVERT: D 256 LYS cc_start: 0.8699 (mttt) cc_final: 0.8424 (mmmt) REVERT: D 285 GLU cc_start: 0.8643 (tp30) cc_final: 0.8401 (tp30) REVERT: E 69 GLU cc_start: 0.9252 (tt0) cc_final: 0.8996 (mt-10) REVERT: E 144 ASP cc_start: 0.7931 (t0) cc_final: 0.6479 (t0) REVERT: E 170 ASP cc_start: 0.8494 (m-30) cc_final: 0.8261 (t70) REVERT: E 184 ASP cc_start: 0.8268 (p0) cc_final: 0.8018 (p0) REVERT: E 205 GLU cc_start: 0.8384 (tt0) cc_final: 0.7758 (tm-30) REVERT: E 208 GLN cc_start: 0.8530 (mt0) cc_final: 0.8305 (mt0) REVERT: E 213 LYS cc_start: 0.8034 (tptp) cc_final: 0.7815 (tptp) REVERT: E 216 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 239 ASP cc_start: 0.8766 (m-30) cc_final: 0.8389 (t0) REVERT: E 245 PHE cc_start: 0.8622 (m-80) cc_final: 0.8372 (m-10) REVERT: E 289 GLN cc_start: 0.8911 (mt0) cc_final: 0.7671 (mt0) REVERT: E 413 TYR cc_start: 0.8572 (m-80) cc_final: 0.7602 (m-80) REVERT: F 130 GLU cc_start: 0.9236 (mt-10) cc_final: 0.9024 (mt-10) REVERT: F 261 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8184 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.3139 time to fit residues: 197.8718 Evaluate side-chains 262 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 160 ASN F 208 GLN F 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.106192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081674 restraints weight = 152930.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.085736 restraints weight = 67095.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.088438 restraints weight = 39326.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.090195 restraints weight = 27512.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091306 restraints weight = 21684.598| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16308 Z= 0.186 Angle : 0.603 6.380 22075 Z= 0.323 Chirality : 0.041 0.162 2609 Planarity : 0.004 0.055 2840 Dihedral : 6.594 55.211 2315 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2047 helix: -0.53 (0.16), residues: 876 sheet: -1.27 (0.29), residues: 271 loop : -1.30 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 191 TYR 0.021 0.001 TYR D 171 PHE 0.013 0.001 PHE F 298 HIS 0.006 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00383 (16307) covalent geometry : angle 0.60255 (22075) hydrogen bonds : bond 0.07122 ( 594) hydrogen bonds : angle 6.27506 ( 1671) Misc. bond : bond 0.00701 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8072 (t80) cc_final: 0.7757 (t80) REVERT: A 170 ASP cc_start: 0.9297 (m-30) cc_final: 0.9033 (m-30) REVERT: A 317 LEU cc_start: 0.7175 (mt) cc_final: 0.6821 (mt) REVERT: B 141 THR cc_start: 0.9465 (t) cc_final: 0.9223 (t) REVERT: B 279 ASP cc_start: 0.8653 (m-30) cc_final: 0.8277 (t0) REVERT: B 293 GLU cc_start: 0.8954 (tt0) cc_final: 0.8455 (tm-30) REVERT: B 393 VAL cc_start: 0.8877 (t) cc_final: 0.8499 (m) REVERT: C 136 LEU cc_start: 0.8816 (tp) cc_final: 0.8561 (tp) REVERT: C 243 ILE cc_start: 0.8920 (mt) cc_final: 0.8611 (mm) REVERT: C 352 ASP cc_start: 0.8536 (p0) cc_final: 0.8207 (p0) REVERT: D 130 GLU cc_start: 0.9033 (tt0) cc_final: 0.8369 (tm-30) REVERT: D 190 SER cc_start: 0.8727 (t) cc_final: 0.8427 (p) REVERT: D 201 ASP cc_start: 0.8729 (m-30) cc_final: 0.8503 (p0) REVERT: D 256 LYS cc_start: 0.8925 (mttt) cc_final: 0.8689 (mmmt) REVERT: D 356 ASP cc_start: 0.8802 (m-30) cc_final: 0.8501 (m-30) REVERT: E 93 TYR cc_start: 0.7994 (t80) cc_final: 0.7721 (t80) REVERT: E 101 ASN cc_start: 0.8507 (m-40) cc_final: 0.8056 (t0) REVERT: E 170 ASP cc_start: 0.8377 (m-30) cc_final: 0.8048 (t70) REVERT: E 239 ASP cc_start: 0.8861 (m-30) cc_final: 0.8550 (t0) REVERT: E 387 LEU cc_start: 0.9165 (tp) cc_final: 0.8955 (tt) REVERT: F 182 TYR cc_start: 0.9167 (t80) cc_final: 0.8614 (t80) REVERT: F 247 CYS cc_start: 0.9169 (m) cc_final: 0.8885 (m) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2905 time to fit residues: 122.0460 Evaluate side-chains 224 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 117 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS D 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.101079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076967 restraints weight = 155053.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080649 restraints weight = 69773.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.083166 restraints weight = 41848.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084737 restraints weight = 29880.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.085790 restraints weight = 24102.438| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16308 Z= 0.222 Angle : 0.592 6.429 22075 Z= 0.314 Chirality : 0.041 0.155 2609 Planarity : 0.003 0.060 2840 Dihedral : 6.501 58.417 2315 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2047 helix: -0.38 (0.16), residues: 902 sheet: -0.92 (0.29), residues: 302 loop : -1.28 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 191 TYR 0.024 0.002 TYR A 93 PHE 0.012 0.001 PHE E 298 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00462 (16307) covalent geometry : angle 0.59229 (22075) hydrogen bonds : bond 0.05194 ( 594) hydrogen bonds : angle 5.95181 ( 1671) Misc. bond : bond 0.00728 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8201 (t80) cc_final: 0.7853 (t80) REVERT: A 317 LEU cc_start: 0.7265 (mt) cc_final: 0.6919 (mt) REVERT: B 141 THR cc_start: 0.9456 (t) cc_final: 0.9233 (t) REVERT: B 188 LYS cc_start: 0.8524 (tttt) cc_final: 0.8099 (tttp) REVERT: B 279 ASP cc_start: 0.8702 (m-30) cc_final: 0.8267 (t0) REVERT: B 293 GLU cc_start: 0.8908 (tt0) cc_final: 0.8682 (tm-30) REVERT: B 352 ASP cc_start: 0.8415 (p0) cc_final: 0.8103 (p0) REVERT: B 393 VAL cc_start: 0.8884 (t) cc_final: 0.8632 (t) REVERT: C 136 LEU cc_start: 0.8866 (tp) cc_final: 0.8626 (tp) REVERT: C 352 ASP cc_start: 0.8473 (p0) cc_final: 0.8110 (p0) REVERT: D 130 GLU cc_start: 0.9064 (tt0) cc_final: 0.8429 (tm-30) REVERT: D 142 MET cc_start: 0.8463 (mtt) cc_final: 0.8034 (mmt) REVERT: D 190 SER cc_start: 0.8798 (t) cc_final: 0.8586 (p) REVERT: D 201 ASP cc_start: 0.8843 (m-30) cc_final: 0.8508 (p0) REVERT: D 256 LYS cc_start: 0.9018 (mttt) cc_final: 0.8813 (mmmt) REVERT: D 356 ASP cc_start: 0.8845 (m-30) cc_final: 0.8559 (m-30) REVERT: E 101 ASN cc_start: 0.8572 (m-40) cc_final: 0.8093 (t0) REVERT: E 170 ASP cc_start: 0.8583 (m-30) cc_final: 0.8147 (t70) REVERT: F 182 TYR cc_start: 0.9168 (t80) cc_final: 0.8737 (t80) REVERT: F 247 CYS cc_start: 0.9137 (m) cc_final: 0.8850 (m) REVERT: F 293 GLU cc_start: 0.8080 (pm20) cc_final: 0.7807 (pm20) REVERT: F 294 ASP cc_start: 0.8930 (m-30) cc_final: 0.7839 (m-30) REVERT: F 342 ASN cc_start: 0.8094 (m-40) cc_final: 0.7876 (m110) outliers start: 1 outliers final: 1 residues processed: 242 average time/residue: 0.2759 time to fit residues: 102.8495 Evaluate side-chains 192 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 182 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 90 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN F 94 ASN F 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.101725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078503 restraints weight = 152812.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082287 restraints weight = 67857.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084807 restraints weight = 40083.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086432 restraints weight = 28219.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087472 restraints weight = 22413.459| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16308 Z= 0.108 Angle : 0.495 5.977 22075 Z= 0.256 Chirality : 0.040 0.155 2609 Planarity : 0.003 0.035 2840 Dihedral : 6.382 58.855 2315 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.12 % Allowed : 0.64 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2047 helix: 0.08 (0.17), residues: 897 sheet: -0.67 (0.30), residues: 287 loop : -1.00 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 191 TYR 0.018 0.001 TYR F 171 PHE 0.007 0.001 PHE C 304 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00234 (16307) covalent geometry : angle 0.49459 (22075) hydrogen bonds : bond 0.04272 ( 594) hydrogen bonds : angle 5.44317 ( 1671) Misc. bond : bond 0.00534 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7156 (mt) cc_final: 0.6882 (mt) REVERT: A 356 ASP cc_start: 0.8361 (t0) cc_final: 0.8140 (p0) REVERT: A 384 MET cc_start: 0.8481 (mtt) cc_final: 0.8237 (mpp) REVERT: B 188 LYS cc_start: 0.8533 (tttt) cc_final: 0.8218 (tttm) REVERT: B 279 ASP cc_start: 0.8622 (m-30) cc_final: 0.8160 (t0) REVERT: B 293 GLU cc_start: 0.8896 (tt0) cc_final: 0.8668 (tm-30) REVERT: B 352 ASP cc_start: 0.8317 (p0) cc_final: 0.8028 (p0) REVERT: B 393 VAL cc_start: 0.8817 (t) cc_final: 0.8478 (t) REVERT: C 136 LEU cc_start: 0.9051 (tp) cc_final: 0.8783 (tp) REVERT: C 181 VAL cc_start: 0.9246 (t) cc_final: 0.8802 (m) REVERT: C 352 ASP cc_start: 0.8520 (p0) cc_final: 0.8137 (p0) REVERT: D 130 GLU cc_start: 0.9023 (tt0) cc_final: 0.8352 (tm-30) REVERT: D 142 MET cc_start: 0.8476 (mtt) cc_final: 0.8018 (mmt) REVERT: D 190 SER cc_start: 0.8821 (t) cc_final: 0.8568 (p) REVERT: D 201 ASP cc_start: 0.8843 (m-30) cc_final: 0.8440 (p0) REVERT: D 356 ASP cc_start: 0.8790 (m-30) cc_final: 0.8479 (m-30) REVERT: E 135 LEU cc_start: 0.7697 (tp) cc_final: 0.7317 (tt) REVERT: E 170 ASP cc_start: 0.8538 (m-30) cc_final: 0.8077 (t70) REVERT: E 175 LYS cc_start: 0.9138 (tttt) cc_final: 0.8740 (ttpp) REVERT: E 387 LEU cc_start: 0.9140 (tp) cc_final: 0.8934 (tt) REVERT: E 413 TYR cc_start: 0.8209 (m-80) cc_final: 0.7690 (m-80) REVERT: F 182 TYR cc_start: 0.9082 (t80) cc_final: 0.8782 (t80) REVERT: F 247 CYS cc_start: 0.9158 (m) cc_final: 0.8902 (m) REVERT: F 261 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.8039 (ttp80) REVERT: F 294 ASP cc_start: 0.8876 (m-30) cc_final: 0.8142 (m-30) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.2591 time to fit residues: 96.0131 Evaluate side-chains 196 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 155 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075366 restraints weight = 154772.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079032 restraints weight = 69891.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.081467 restraints weight = 41872.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083059 restraints weight = 29961.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.083932 restraints weight = 24049.606| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16308 Z= 0.204 Angle : 0.561 6.399 22075 Z= 0.292 Chirality : 0.040 0.151 2609 Planarity : 0.003 0.032 2840 Dihedral : 6.503 62.549 2315 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2047 helix: -0.06 (0.17), residues: 906 sheet: -0.50 (0.29), residues: 307 loop : -1.18 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 261 TYR 0.012 0.001 TYR F 96 PHE 0.009 0.001 PHE B 304 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00424 (16307) covalent geometry : angle 0.56052 (22075) hydrogen bonds : bond 0.03847 ( 594) hydrogen bonds : angle 5.54164 ( 1671) Misc. bond : bond 0.00921 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7227 (mt) cc_final: 0.6968 (mt) REVERT: A 384 MET cc_start: 0.8621 (mtt) cc_final: 0.8336 (mpp) REVERT: B 141 THR cc_start: 0.9433 (t) cc_final: 0.9219 (t) REVERT: B 188 LYS cc_start: 0.8575 (tttt) cc_final: 0.8201 (tttp) REVERT: B 279 ASP cc_start: 0.8674 (m-30) cc_final: 0.8221 (t0) REVERT: B 352 ASP cc_start: 0.8420 (p0) cc_final: 0.8097 (p0) REVERT: B 363 MET cc_start: 0.8428 (mtm) cc_final: 0.8219 (ptp) REVERT: B 393 VAL cc_start: 0.8852 (t) cc_final: 0.8589 (t) REVERT: C 136 LEU cc_start: 0.9036 (tp) cc_final: 0.8772 (tp) REVERT: C 181 VAL cc_start: 0.9309 (t) cc_final: 0.8853 (m) REVERT: C 352 ASP cc_start: 0.8621 (p0) cc_final: 0.8267 (p0) REVERT: D 130 GLU cc_start: 0.9073 (tt0) cc_final: 0.8430 (tm-30) REVERT: D 142 MET cc_start: 0.8609 (mtt) cc_final: 0.8132 (mmt) REVERT: D 190 SER cc_start: 0.8900 (t) cc_final: 0.8668 (p) REVERT: D 356 ASP cc_start: 0.8831 (m-30) cc_final: 0.8515 (m-30) REVERT: E 170 ASP cc_start: 0.8682 (m-30) cc_final: 0.8161 (t70) REVERT: F 216 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8050 (tm-30) REVERT: F 247 CYS cc_start: 0.9209 (m) cc_final: 0.8967 (m) REVERT: F 294 ASP cc_start: 0.8867 (m-30) cc_final: 0.7827 (m-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2681 time to fit residues: 92.7718 Evaluate side-chains 179 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 92 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.0670 chunk 175 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078105 restraints weight = 154172.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.081825 restraints weight = 67546.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084286 restraints weight = 39634.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085857 restraints weight = 27869.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.086876 restraints weight = 22148.335| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16308 Z= 0.117 Angle : 0.484 6.074 22075 Z= 0.252 Chirality : 0.040 0.154 2609 Planarity : 0.003 0.040 2840 Dihedral : 6.388 64.338 2315 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 2047 helix: 0.29 (0.17), residues: 901 sheet: -0.30 (0.30), residues: 292 loop : -0.91 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 261 TYR 0.011 0.001 TYR F 96 PHE 0.009 0.001 PHE B 304 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00250 (16307) covalent geometry : angle 0.48429 (22075) hydrogen bonds : bond 0.03490 ( 594) hydrogen bonds : angle 5.19186 ( 1671) Misc. bond : bond 0.00628 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7091 (mt) cc_final: 0.6864 (mt) REVERT: A 356 ASP cc_start: 0.8508 (p0) cc_final: 0.8285 (m-30) REVERT: A 384 MET cc_start: 0.8675 (mtt) cc_final: 0.8324 (mpp) REVERT: B 140 PHE cc_start: 0.7735 (t80) cc_final: 0.6613 (t80) REVERT: B 141 THR cc_start: 0.9419 (t) cc_final: 0.9122 (t) REVERT: B 142 MET cc_start: 0.8332 (mpp) cc_final: 0.8018 (mpp) REVERT: B 188 LYS cc_start: 0.8547 (tttt) cc_final: 0.8178 (tttp) REVERT: B 352 ASP cc_start: 0.8410 (p0) cc_final: 0.8103 (p0) REVERT: C 181 VAL cc_start: 0.9312 (t) cc_final: 0.8853 (m) REVERT: C 352 ASP cc_start: 0.8544 (p0) cc_final: 0.8186 (p0) REVERT: D 130 GLU cc_start: 0.9080 (tt0) cc_final: 0.8412 (tm-30) REVERT: D 142 MET cc_start: 0.8671 (mtt) cc_final: 0.8132 (mmt) REVERT: D 190 SER cc_start: 0.9061 (t) cc_final: 0.8685 (p) REVERT: D 201 ASP cc_start: 0.9063 (m-30) cc_final: 0.8468 (p0) REVERT: D 356 ASP cc_start: 0.8820 (m-30) cc_final: 0.8478 (m-30) REVERT: E 101 ASN cc_start: 0.8468 (m-40) cc_final: 0.7963 (t0) REVERT: E 135 LEU cc_start: 0.7885 (tt) cc_final: 0.7674 (tp) REVERT: E 170 ASP cc_start: 0.8698 (m-30) cc_final: 0.8143 (t70) REVERT: E 413 TYR cc_start: 0.8644 (m-80) cc_final: 0.8432 (m-80) REVERT: F 247 CYS cc_start: 0.9253 (m) cc_final: 0.8993 (m) REVERT: F 294 ASP cc_start: 0.8800 (m-30) cc_final: 0.8177 (m-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2666 time to fit residues: 94.6971 Evaluate side-chains 180 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 146 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.100763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077763 restraints weight = 154406.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.081468 restraints weight = 67329.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.083912 restraints weight = 39329.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.085482 restraints weight = 27604.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.086485 restraints weight = 21919.977| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16308 Z= 0.125 Angle : 0.489 6.058 22075 Z= 0.254 Chirality : 0.040 0.150 2609 Planarity : 0.003 0.028 2840 Dihedral : 6.311 65.740 2315 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2047 helix: 0.36 (0.17), residues: 909 sheet: -0.11 (0.30), residues: 292 loop : -0.86 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 100 TYR 0.012 0.001 TYR F 96 PHE 0.016 0.001 PHE A 140 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00270 (16307) covalent geometry : angle 0.48931 (22075) hydrogen bonds : bond 0.03255 ( 594) hydrogen bonds : angle 5.12196 ( 1671) Misc. bond : bond 0.00710 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7122 (mt) cc_final: 0.6842 (mt) REVERT: B 140 PHE cc_start: 0.7678 (t80) cc_final: 0.7393 (t80) REVERT: B 188 LYS cc_start: 0.8457 (tttt) cc_final: 0.8159 (tttp) REVERT: B 352 ASP cc_start: 0.8362 (p0) cc_final: 0.8019 (p0) REVERT: C 181 VAL cc_start: 0.9327 (t) cc_final: 0.8865 (m) REVERT: C 352 ASP cc_start: 0.8505 (p0) cc_final: 0.8145 (p0) REVERT: D 130 GLU cc_start: 0.9050 (tt0) cc_final: 0.8405 (tm-30) REVERT: D 142 MET cc_start: 0.8675 (mtt) cc_final: 0.8074 (mmt) REVERT: D 190 SER cc_start: 0.9078 (t) cc_final: 0.8765 (p) REVERT: D 356 ASP cc_start: 0.8781 (m-30) cc_final: 0.8442 (m-30) REVERT: E 101 ASN cc_start: 0.8430 (m-40) cc_final: 0.7942 (t0) REVERT: E 170 ASP cc_start: 0.8707 (m-30) cc_final: 0.8199 (t70) REVERT: F 182 TYR cc_start: 0.8836 (t80) cc_final: 0.8389 (t80) REVERT: F 294 ASP cc_start: 0.8444 (m-30) cc_final: 0.8100 (m-30) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.2560 time to fit residues: 87.4575 Evaluate side-chains 175 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 113 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 160 optimal weight: 0.0770 chunk 63 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076781 restraints weight = 156135.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080411 restraints weight = 68009.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.082832 restraints weight = 40001.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084374 restraints weight = 28183.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085249 restraints weight = 22458.258| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16308 Z= 0.157 Angle : 0.513 6.146 22075 Z= 0.268 Chirality : 0.040 0.149 2609 Planarity : 0.003 0.032 2840 Dihedral : 6.390 67.363 2315 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2047 helix: 0.30 (0.17), residues: 918 sheet: 0.00 (0.29), residues: 307 loop : -0.98 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.012 0.001 TYR F 96 PHE 0.009 0.001 PHE B 304 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00333 (16307) covalent geometry : angle 0.51274 (22075) hydrogen bonds : bond 0.03221 ( 594) hydrogen bonds : angle 5.16043 ( 1671) Misc. bond : bond 0.00640 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ASN cc_start: 0.8518 (m-40) cc_final: 0.8104 (t0) REVERT: A 317 LEU cc_start: 0.7096 (mt) cc_final: 0.6567 (mt) REVERT: B 188 LYS cc_start: 0.8403 (tttt) cc_final: 0.8189 (tttm) REVERT: B 352 ASP cc_start: 0.8408 (p0) cc_final: 0.8073 (p0) REVERT: C 352 ASP cc_start: 0.8435 (p0) cc_final: 0.8075 (p0) REVERT: D 130 GLU cc_start: 0.9151 (tt0) cc_final: 0.8473 (tm-30) REVERT: D 142 MET cc_start: 0.8732 (mtt) cc_final: 0.8134 (mmt) REVERT: D 356 ASP cc_start: 0.8795 (m-30) cc_final: 0.8457 (m-30) REVERT: E 135 LEU cc_start: 0.7983 (tt) cc_final: 0.7414 (tt) REVERT: E 170 ASP cc_start: 0.8797 (m-30) cc_final: 0.8272 (t70) REVERT: F 182 TYR cc_start: 0.8942 (t80) cc_final: 0.8604 (t80) REVERT: F 294 ASP cc_start: 0.8306 (m-30) cc_final: 0.7984 (m-30) REVERT: F 303 GLU cc_start: 0.7508 (mp0) cc_final: 0.7264 (mp0) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2542 time to fit residues: 85.1112 Evaluate side-chains 175 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072941 restraints weight = 154503.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.076562 restraints weight = 69868.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.078971 restraints weight = 42147.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.080528 restraints weight = 30451.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081535 restraints weight = 24679.708| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16308 Z= 0.197 Angle : 0.547 6.208 22075 Z= 0.286 Chirality : 0.040 0.146 2609 Planarity : 0.003 0.032 2840 Dihedral : 6.534 69.281 2315 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2047 helix: 0.14 (0.17), residues: 908 sheet: -0.09 (0.29), residues: 319 loop : -0.95 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.012 0.001 TYR A 96 PHE 0.017 0.001 PHE A 140 HIS 0.024 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00412 (16307) covalent geometry : angle 0.54731 (22075) hydrogen bonds : bond 0.03368 ( 594) hydrogen bonds : angle 5.28508 ( 1671) Misc. bond : bond 0.00777 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ASN cc_start: 0.8554 (m-40) cc_final: 0.8106 (t0) REVERT: B 188 LYS cc_start: 0.8448 (tttt) cc_final: 0.8234 (tttm) REVERT: B 352 ASP cc_start: 0.8461 (p0) cc_final: 0.8138 (p0) REVERT: B 363 MET cc_start: 0.8561 (mtm) cc_final: 0.8287 (ptp) REVERT: C 352 ASP cc_start: 0.8490 (p0) cc_final: 0.8146 (p0) REVERT: D 130 GLU cc_start: 0.9153 (tt0) cc_final: 0.8421 (tm-30) REVERT: D 142 MET cc_start: 0.8780 (mtt) cc_final: 0.8145 (mmt) REVERT: D 286 LEU cc_start: 0.9542 (tp) cc_final: 0.9342 (tt) REVERT: D 356 ASP cc_start: 0.8856 (m-30) cc_final: 0.8493 (m-30) REVERT: E 135 LEU cc_start: 0.7873 (tt) cc_final: 0.7560 (tt) REVERT: E 170 ASP cc_start: 0.8886 (m-30) cc_final: 0.8345 (t70) REVERT: F 182 TYR cc_start: 0.9019 (t80) cc_final: 0.8592 (t80) REVERT: F 294 ASP cc_start: 0.8279 (m-30) cc_final: 0.7982 (m-30) REVERT: F 303 GLU cc_start: 0.7611 (mp0) cc_final: 0.7331 (mp0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2663 time to fit residues: 86.9344 Evaluate side-chains 168 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 107 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.098008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074094 restraints weight = 153710.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077802 restraints weight = 68283.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080254 restraints weight = 40596.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081826 restraints weight = 28983.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.082812 restraints weight = 23316.573| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16308 Z= 0.102 Angle : 0.477 6.094 22075 Z= 0.247 Chirality : 0.040 0.152 2609 Planarity : 0.003 0.031 2840 Dihedral : 6.352 69.823 2315 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 2047 helix: 0.47 (0.17), residues: 911 sheet: 0.08 (0.31), residues: 278 loop : -0.71 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.011 0.001 TYR F 96 PHE 0.012 0.001 PHE A 245 HIS 0.011 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00224 (16307) covalent geometry : angle 0.47682 (22075) hydrogen bonds : bond 0.03069 ( 594) hydrogen bonds : angle 4.93665 ( 1671) Misc. bond : bond 0.00624 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8081 (t80) cc_final: 0.7797 (t80) REVERT: A 315 ASN cc_start: 0.8555 (m-40) cc_final: 0.8113 (t0) REVERT: A 317 LEU cc_start: 0.7064 (mt) cc_final: 0.6462 (mt) REVERT: B 188 LYS cc_start: 0.8426 (tttt) cc_final: 0.8209 (tttm) REVERT: B 352 ASP cc_start: 0.8411 (p0) cc_final: 0.8082 (p0) REVERT: B 363 MET cc_start: 0.8519 (mtm) cc_final: 0.8258 (ptp) REVERT: C 320 GLU cc_start: 0.8728 (pp20) cc_final: 0.8409 (pp20) REVERT: C 352 ASP cc_start: 0.8435 (p0) cc_final: 0.8091 (p0) REVERT: D 130 GLU cc_start: 0.9129 (tt0) cc_final: 0.8445 (tm-30) REVERT: D 142 MET cc_start: 0.8781 (mtt) cc_final: 0.8165 (mmt) REVERT: D 356 ASP cc_start: 0.8792 (m-30) cc_final: 0.8442 (m-30) REVERT: E 170 ASP cc_start: 0.8823 (m-30) cc_final: 0.8281 (t70) REVERT: E 205 GLU cc_start: 0.8175 (pp20) cc_final: 0.7253 (pp20) REVERT: E 413 TYR cc_start: 0.8524 (m-80) cc_final: 0.8006 (m-80) REVERT: F 182 TYR cc_start: 0.8975 (t80) cc_final: 0.8551 (t80) REVERT: F 294 ASP cc_start: 0.8321 (m-30) cc_final: 0.7996 (m-30) REVERT: F 303 GLU cc_start: 0.7573 (mp0) cc_final: 0.7287 (mp0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2604 time to fit residues: 88.2358 Evaluate side-chains 175 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 100 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.098620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075214 restraints weight = 153721.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078899 restraints weight = 67523.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081321 restraints weight = 39655.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082865 restraints weight = 28029.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.083880 restraints weight = 22392.375| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16308 Z= 0.149 Angle : 0.509 6.231 22075 Z= 0.266 Chirality : 0.040 0.146 2609 Planarity : 0.003 0.031 2840 Dihedral : 6.395 70.299 2315 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 2047 helix: 0.38 (0.17), residues: 912 sheet: 0.06 (0.30), residues: 302 loop : -0.77 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.011 0.001 TYR F 96 PHE 0.009 0.001 PHE B 304 HIS 0.011 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00314 (16307) covalent geometry : angle 0.50860 (22075) hydrogen bonds : bond 0.03128 ( 594) hydrogen bonds : angle 5.08722 ( 1671) Misc. bond : bond 0.00705 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.62 seconds wall clock time: 84 minutes 44.74 seconds (5084.74 seconds total)